[Biocorba-l] Biocorba IDL

[Jason Eric Stajich]

Alan - 

I'm really happy to have you using the idl.  I have a couple of small side
projects using biocorba, but am still trying to find the appropriate place
to really focus on using it.  Ewan and I have discussed biocorba as an
Ensembl bridge in the future, but I'm not sure what the timeframe will be.  
Needless to say the idl has not then been tested much beyond our initial
efforts.

I think we need to have a central idl location - previously it has been in
the bioperl-corba-server cvs module, but I think we need to be less
project dependent.  I just put in a cvs repository for biocorba called
biocorba-idls.  If you want to commit changes yourself we'll need to get
you setup with a cvs account, otherwise I'll go ahead see about
incorperating these changes.

Please let the list know how your server performs and other
criticisms/changes to the idl that ought to be discussed.

Jason

On Thu, 19 Oct 2000, Alan Robinson wrote:

> Hi,
> 
> I'm writing a Biocorba server currently (planned to be released next
> week), and whilst working with the Biocorba IDL I've come across the
> following issues:
> 
> The following are errors in the BioCorba.idl available from the web site.
> Unless these are corrected, the IDL won't compile with an IDL compiler.
> 
> The main problem is that all the IDL sequences have been defined
> incorrectly. Plus an exception is declared wrongly. 
> 
> diff BioCorba.idl BioCorbaFixed.idl:
> 
> 52c52
> <      exception RequestTooLarge { string reason,long suggested_size; }; 
> ---
> >      exception RequestTooLarge { string reason; long suggested_size; }; 
> 
> 144c144
> <      typedef sequence  stringList;
> ---
> >      typedef sequence<string>  stringList;
> 
> 150c150
> <      typedef sequence  NameValueSetList;
> ---
> >      typedef sequence<NameValueSet>  NameValueSetList;
> 
> 169c169
> <      typedef sequence  SeqFeatureList;
> ---
> >      typedef sequence<SeqFeature> SeqFeatureList;
> 
> 213c213
> <      typedef sequence  primaryidList;
> ---
> >      typedef sequence<primaryid>  primaryidList;
> 
> 223,224c224,225
> <      typedef sequence  SeqList;
> <      typedef sequence  PrimarySeqList;
> ---
> >      typedef sequence<Seq>  SeqList;
> >      typedef sequence<PrimarySeq>  PrimarySeqList;
> 
> 
> Next, there is an inconsistency in variable type: In the BioEnv interface,
> the methods all define the 'version' variable as being a string. However,
> the PrimarySeqDB interface defines the database version as a 'short'.
> 
> 
> The following are suggestions (***YMMV***):
> 
> The module is defined as org::Biocorba::Seqcore so "we look good in Java".
> Stylisticly, it should be org::biocorba::seqcore (Java packages are not
> capitalised, but Java objects are).
> 
> However, wouldn't it make more sense for the module to be just "Bio"? Then
> it would fit better with bioperl and make life easier for C interface
> users.
> 
> The BioEnv interface defines methods to fetch a SeqDB by name, but it
> doesn't allow you to ask what SeqDB names it holds. A 'stringList
> get_SeqDB_names();' method would be useful here.
> 
> For the iterators, it would be convenient to have a 'reset()' method that
> takes you back to the first item of the iterator, so that if we want to
> cycle over the values again, we don't have to re-create the object.
> 
> The only SeqTypes defined are PROTEIN, DNA and RNA. It would be useful to
> have also CIRCULAR_DNA, CIRCULAR_RNA and XXX (e.g. see Ac#:S47134).
> 
> The exception "DoesNotExist" is not thrown by any methods of the IDL.
> 
> 
> The following is heading into fluff territory:
> 
> In the PrimarySeqDB interface, the methods 'database_name()' and
> 'database_version()' could be shortened to 'name()' and 'version' for
> consistency.
> 
> In the documentation for the iterators: 
> 
>   boolean has_more(); // returns 1 when next_seq will give an object.
> 
> Technically '1' is not a boolean. If the method really returns '1', it
> should be a 'short' being returned.
> 
> 
> cheers,
> al
> 
> 
> --
> ============================================================
> Alan J. Robinson, D.Phil.             Tel:+44-(0)1223 494444
> European Bioinformatics Institute     Fax:+44-(0)1223 494468
> EMBL Outstation - Hinxton             Email:  alan@ebi.ac.uk
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD, UK                http://industry.ebi.ac.uk/~alan/
> ============================================================
> 
> 
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> 

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/